Methods and systems for simultaneous real-time monitoring of optical signals from multiple sources

Abstract

Methods and systems for real-time monitoring of optical signals from arrays of signal sources, and particularly optical signal sources that have spectrally different signal components. Systems include signal source arrays in optical communication with optical trains that direct excitation radiation to and emitted signals from such arrays and image the signals onto detector arrays, from which such signals may be subjected to additional processing.

1. A method of analyzing a plurality of signal sources on a substrate, comprising:
 providing at least first plurality and second plurality of adjacent signal sources on a substrate, wherein the first plurality of signal sources is in a first row, the second plurality of signal sources is in a second row, and the first row and second row are substantially parallel; 
 selectively directing excitation radiation at the first plurality and second plurality of signal sources while not substantially illuminating space between the first plurality and second plurality of signal sources,
 wherein a first linear illumination profile illuminates the first plurality of signal sources, and a second linear illumination profile simultaneously illuminates the second plurality of signal sources, and the distance between the first illumination profile and the second illumination profile corresponds to the distance between the first row and the second row of signal sources. 
 
 
     
     
       2. The method of  claim 1  wherein the first plurality and second plurality of signal sources comprise chemical or biochemical reactions. 
     
     
       3. The method of  claim 2  wherein the chemical or biochemical reactions include immunoassays, enzymatic assays, receptor assays, nucleic acid hybridization assays, nucleic acid synthesis reactions, cellular assays. 
     
     
       4. The method of  claim 2  wherein the chemical or biochemical reactions comprise single molecule analysis. 
     
     
       5. The method of  claim 2  wherein the chemical or biochemical reactions comprise nucleic acid sequencing reactions. 
     
     
       6. The method of  claim 2  wherein the chemical or biochemical reactions result in one or more of the consumption, production and conversion of a material, that is capable of generating an optically detectable signal. 
     
     
       7. The method of  claim 1  wherein the signal sources comprise wells, depressions, channels, or other structures that retain reaction constituents. 
     
     
       8. The method of  claim 1  wherein the signal sources comprise zones that are maintained discrete from other regions by chemical barriers. 
     
     
       9. The method of  claim 1  wherein the substrate comprises an optically transparent layer upon which the signal sources are disposed. 
     
     
       10. The method of  claim 1  wherein the signal sources are provided on the substrate in an array format, having more than 10,000 signal sources. 
     
     
       11. The method of  claim 10  wherein the signal sources are regularly spaced on the substrate. 
     
     
       12. The method of  claim 1  wherein the spacing between the signal sources is from about 0.1 micron to about 10 micron. 
     
     
       13. The method of  claim 1  wherein signal sources comprise zero mode waveguides. 
     
     
       14. The method of  claim 1  wherein the spacing between the signal sources is from about 0.8 micron to about 3 micron. 
     
     
       15. The method of  claim 1  further comprising optically monitoring signals from the first and second signal sources. 
     
     
       16. The method of  claim 15  wherein the signals are concurrently optically monitored in real-time. 
     
     
       17. The method of  claim 16  wherein the signals are indicative of the reaction or conversion of a chemical, biochemical, or biological reaction. 
     
     
       18. The method of  claim 1  wherein the first and second linear profiles are produced using a lens or a holographic optical element (HOE). 
     
     
       19. The method of  claim 1  wherein the first and second linear profiles are shaped using a spatial filter. 
     
     
       20. The method of  claim 1  wherein the first and second linear profiles have an aspect ratio (length:width) of greater than 100.